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<h2>Summary Section</h2>


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This section shows the projects selected from the Project list in
the left panel. Use the links to load projects and/or annotation to the database,
remove projects, or alter project parameters.
<p>
If new sequences are loaded, MUMmer or BLAT alignments will need to be run again.
Note that re-loading sequences for a project is the same as removing
the project and loading it again. 
<p>
If new annotation is loaded (but sequences stay the same), then synteny should
be recomputed but the existing MUMmer of BLAT files can still be used. 
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<h2>Available Synteny Section</h2>
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This section shows a table with the status of alignments between
the selected projects. (Only projects loaded to the database are shown.)
<p>
Each cell in the table represents a pair of projects (labeled on the
rows and columns) and the cell contains a status code showing
 whether or not that pair has been aligned (codes are listed below). Note that the table
actually shows each pair twice, but only the lower cells are activated.
<p>
Clicking on a cell selects that pair of projects (the cell then highlights in yellow). 
Alignment and synteny may then be computed or viewed for that particular pair, using
the function buttons (described below). If no cell is selected, you can still
use some of the function buttons, which apply to all the cells. 
</div>

<p>
<b>Status Codes:</b>
<br>
<table border='1' cellpadding='5' rules=all>
<tr>
	<td align="left">
		<b>Symbol</b>
	</td>
	<td align="left" >
		<b>Description</b>
	</td>
</tr>
<tr>
	<td align="left" valign="top">
		&#10004;
	</td>
	<td align="left"  valign="top" width="550" >
		Synteny for this project pair is ready to view.
	</td>
</tr>
<tr>
	<td align="left" valign="top">
		A
	</td>
	<td align="left"  valign="top" width="550" >
		The alignment (MUMmer or BLAT) has been performed but the anchors have not been
		loaded and the synteny computation has not been run. This status occurs if
		a pair is completed but then annotations are re-loaded for one of the projects. 
	</td>
</tr>
<tr>
	<td align="left" valign="top">
		&lt;empty cell&gt;
	</td>
	<td align="left"  valign="top" width="550" >
		The alignment has not been started.
	</td>
</tr>
</table>
<p>
<b> CPUs parameter:</b> Enter the maximum number of CPUs you wish to use for an alignment. SyMAP will use 
up to that number (but may use fewer, depending on the number of sequences being aligned).
<p>
<b>Function Buttons:</b>
<br>
<table border='1' cellpadding='5' rules=all>
<tr>
	<td align="left">
		<b>Label</b>
	</td>
	<td align="left" >
		<b>Description</b>
	</td>
</tr>
<tr>
	<td align="center" valign="top" colspan=2>
		<i>Alignment & Synteny</i> 
	</td>
</tr>
<tr>
	<td align="left" valign="top">
		Selected Pair
	</td>
	<td align="left"  valign="top" width="550" >
		Run (or complete) the alignment & synteny computation for the selected project pair. 
		If the pair is already complete, the button label changes to "Re-do", and 
		the function is to re-run the synteny computation only. If you wish to re-run
		the BLAT or MUMmer alignment also, first use the "Clear Pair" function. 
	</td>
</tr>
<tr>
	<td align="left" valign="top">
		All Pairs
	</td>
	<td align="left"  valign="top" width="550" >
		Run (or complete) the synteny computation for all pairs in the Available Syntenies table.  
	</td>
</tr>
<tr>
	<td align="left" valign="top">
		Parameters
	</td>
	<td align="left"  valign="top" width="550" >
		Set alignment & synteny parameters (has its own help window). 
	</td>
</tr>
<tr>
	<td align="left" valign="top">
		Clear Pair
	</td>
	<td align="left"  valign="top" width="550" >
		Fully reset the selected pair, removing its synteny results and its MUMmer or BLAT 
		alignment files. 
	</td>
</tr>
<tr>
	<td align="center" valign="top" colspan=2>
		<i>Display for Selected Pair</i> 
	</td>
</tr>
<tr>
	<td align="left" valign="top">
		Dot Plot
	</td>
	<td align="left"  valign="top" width="550" >
		Show a dotplot display for the selected pair.
	</td>
</tr>
<tr>
	<td align="left" valign="top">
		Block View
	</td>
	<td align="left"  valign="top" width="550" >
		A linear display showing synteny blocks of one project aligned
		next to the chromosomes of the other.   
	</td>
</tr>
<tr>
	<td align="left" valign="top">
		Circle View
	</td>
	<td align="left"  valign="top" width="550" >
		Circular display (Circos-style) 
	</td>
</tr>
<tr>
	<td align="left" valign="top">
		Summary
	</td>
	<td align="left"  valign="top" width="550" >
		Show overall information and statistics for the pair alignment (sequence pairs only)
	</td>
</tr>
<tr>
	<td align="center" valign="top" colspan=2>
		<i>Display for All Projects</i> 
	</td>
</tr>
<tr>
	<td align="left" valign="top">
		Chromosome Explorer
	</td>
	<td align="left"  valign="top" width="550" >
		Show the Explorer, allowing selected chromosome sets to be viewed in
		dot plot, side-by-side, circular, or 3D displays (the latter only
		for supported platforms.)
	</td>
</tr>
<tr>
	<td align="center" valign="top" colspan=2>
		<i>Queries</i> 
	</td>
</tr>
<tr>
	<td align="left" valign="top">
		SyMAP Queries
	</td>
	<td align="left"  valign="top" width="550" >
		Show the SyMAP Query interface, for locating shared genes, orphans, putative gene families,
		and other valuable synteny-derived information.
	</td>
</tr>
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